Actually they BOTH need to be done. The firing order needs to be re-pinned to the correct order and the firing order in the diagnostics tab should be changed. The firing order will not put the injectors and coils into the correct order, but it will correct the firing order in the tune so that the PCM will flag the correct cylinder when you have an injector/coil/misfire related code. If you do not correct the diagnostic side, the PCM will flag the wrong cylinder and you will go crazy trying to diagnose say a p0307 misfire, on cylinder 7 it would actually be cylinder 4 with the problem.
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